I have a CF card taken from my A1200 and connected to an OSX laptop using a USB adapter. I have the CF card working in FS-UAE and it boots just fine and behaves just like my A1200.

However, I want to copy software from my OSX hard drive so I added a directory as a HD in the config, but FS-UAE insists on prioritising the directory as a boot device over the CF card.

I have entries for hard_drive_0_priority and hard_drive_1_priority in my config file but no matter what I put for each, the directory is always the boot device. I know my config file is being used as I can comment out the directory HD from it and it then boots fine from the CF card.

The CF card will have its own priorities set in the RDB, independent of the config file priorities. You need to set them with HDToolbox or whatever tool you use for dealing with partitions. You can always go to the early startup menu and manually choose a partition to boot from...